In the construction of the database we have aimed to address
the following:

Support frequent updates -The
number of new structures in the PDB is growing rapidly. In
order to utilize these structures, frequent updates are required.
In contrast to manual procedures which require significant time and
effort per update, generation of the PSMDB database is fully automatic
thereby facilitating frequent database updates.

Consider
both protein and ligand structural redundancy - In our database, two complexes are
considered redundant if they share a similar protein and ligand (our protein - small-molecule non-redundant set).
This allows the database to contain structural information for the same
protein bound to several different ligands (and vice-versa).
Additionally, for completeness, the database contains a set of
non-redundant complexes when only protein structural redundancy is considered (our protein non-redundant set). The following images demonstrate the structural redundancy of the protein complexes in the PDB compared to the PSMDB.

Efficient handling of covalent bonds -Many
protein complexes contain covalently bound ligands. Typically,
protein-ligand databases discard these complexes; however, the PSMDB
simply removes the covalently bound ligand from the complex, retaining
any non-covalently bound ligands. This increases the number of usable
complexes in the database.

Separate complexes into protein and ligand files -The
PSMDB contains individual structure files for both the protein and all
non-covalently bound ligands. The unbound proteins are in PDB format while the individual ligands are in SDF format (in their native coordinate frame).